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Full-Text Articles in Plant Sciences
Genotyping Of The Fragrance Allele In Rice, Louis Mt Bradbury, Robert J. Henry, Qingsheng Jin, Russell F. Reinke, Daniel Le Waters
Genotyping Of The Fragrance Allele In Rice, Louis Mt Bradbury, Robert J. Henry, Qingsheng Jin, Russell F. Reinke, Daniel Le Waters
Adjunct Associate Professor Daniel LE Waters
We have previously determined that fragrance in rice, a recessive trait, is due to a large deletion (8bp) and 3 SNP’s in a gene on chromosome 8 which encodes a putative betaine aldehyde dehydrogenase 2 (BAD2). This mutation results in the formation of a truncated BAD2 enzyme because of the creation of an in-frame termination signal 800bp before that of the wild type. Because this truncated BAD2 is missing key binding domains, it is unlikely that it is capable of acting upon the target substrate and this leads to an accumulation of the principal fragrant molecule, 2-acetyl-1-pyrroline. Here we utilise …
Rice Genome Sequence Accelerates The Discovery Of Commercially Important Genes And Polymorphisms, Daniel Le Waters, Louis Mt Bradbury, Russell F. Reinke, Melissa A. Fitzgerald, Qingsheng Jin, Robert J. Henry
Rice Genome Sequence Accelerates The Discovery Of Commercially Important Genes And Polymorphisms, Daniel Le Waters, Louis Mt Bradbury, Russell F. Reinke, Melissa A. Fitzgerald, Qingsheng Jin, Robert J. Henry
Adjunct Associate Professor Daniel LE Waters
Traditionally, identification of genes which control important traits has been labour intensive and time consuming. We have demonstrated the annotated rice genome sequence used in combination with re-sequencing by PCR greatly facilitates the discovery of both genes and polymorphisms within genes, which control commercially important traits. Identification of the gene which controls fragrance was achieved using a relatively small mapping population of 168 F2 individuals. Analysis of the recombination data and the relatively large tract (385 kbp) of annotated genome sequence between the flanking markers revealed a candidate gene in this region which plausibly explained the known biochemistry of fragrance. …
Scaming: An Efficient High Throughput Approach To Discovery And Analysis Of Snps For Genotyping Of Tropical Crop Species, Frances G. Eliott, Giovanni M. Cordeiro, Nicole F. Rice, James K. Cronin, Daniel Le Waters, Peter C. Bundock, Stirling Bowen, Robert J. Henry
Scaming: An Efficient High Throughput Approach To Discovery And Analysis Of Snps For Genotyping Of Tropical Crop Species, Frances G. Eliott, Giovanni M. Cordeiro, Nicole F. Rice, James K. Cronin, Daniel Le Waters, Peter C. Bundock, Stirling Bowen, Robert J. Henry
Adjunct Associate Professor Daniel LE Waters
Model organisms have well established genetic marker tools. However, genotyping of the wide range of agricultural and food species requires the discovery of genetic variations in each species that can be used to distinguish genotypes. Single Nucleotide Polymorphisms (SNPs) are the basis of most high throughput genetic analysis technologies. We have developed a generic approach to the discovery and analysis of SNPs in non-model organisms. SNP Characterisation and Mapping in Genomes (SCAMinG) has been developed from mutation detection based on enzymatic cleavage of DNA heteroduplexes as applied to naturally occurring genetic variation (ecoTILLinG). Our protocol involves application of high throughput …
Evaluation Of Starch Granule Morphology In Wild Relatives Of Rice Using Scanning Electron Microscopy, Shabana Kasem, Daniel Le Waters, Nicole F. Rice, Robert J. Henry
Evaluation Of Starch Granule Morphology In Wild Relatives Of Rice Using Scanning Electron Microscopy, Shabana Kasem, Daniel Le Waters, Nicole F. Rice, Robert J. Henry
Adjunct Associate Professor Daniel LE Waters
Rice grains exhibit unique starch properties and these properties differ among varieties. Starch granule morphology influences the physicochemical characteristics of starch and granule shape/size are a contributing factor in starch functional properties. Wild rice relatives represent a diverse range of material that may be useful for the identification of novel end-products or identify new germplasm for breeding programs. Comparative scanning electron microscopy studies can reveal differences in starch granule morphology between species. This study presents a qualitative evaluation of starch granule morphology of 19 spp. from four different genera (Oryza, Potamophila, Microlaena and Zizania) belonging to two different tribes (Oryzeae, …
Improving Cereals For Human Health, Shane R. Mcintosh, Daniel Le Waters, Louis Mt Bradbury, Timothy L. Fitzgerald, Robert J. Henry
Improving Cereals For Human Health, Shane R. Mcintosh, Daniel Le Waters, Louis Mt Bradbury, Timothy L. Fitzgerald, Robert J. Henry
Adjunct Associate Professor Daniel LE Waters
No abstract provided.
Competitive Allele Specific Pcr Molecular Markers For Rice [Oryza Sativa] Starch Gelatinisation Temperature, Daniel Le Waters, Robert J. Henry, Russell F. Reinke
Competitive Allele Specific Pcr Molecular Markers For Rice [Oryza Sativa] Starch Gelatinisation Temperature, Daniel Le Waters, Robert J. Henry, Russell F. Reinke
Adjunct Associate Professor Daniel LE Waters
No abstract provided.
Improving Rice For Human Health, Daniel Le Waters, Shane R. Mcintosh, Louis Mt Bradbury, Timothy L. Fitzgerald, Robert J. Henry
Improving Rice For Human Health, Daniel Le Waters, Shane R. Mcintosh, Louis Mt Bradbury, Timothy L. Fitzgerald, Robert J. Henry
Adjunct Associate Professor Daniel LE Waters
No abstract provided.
Cel I And The Email Mutation Scanning Assay, Michael J. Cross, Daniel Le Waters, L Slade Lee, Robert J. Henry
Cel I And The Email Mutation Scanning Assay, Michael J. Cross, Daniel Le Waters, L Slade Lee, Robert J. Henry
Adjunct Associate Professor Daniel LE Waters
Scanning for unknown mutations has been advanced by mismatch cleavage techniques. Pioneering methods include the use of ribonucleases, chemical cleavage of mismatch (CCM) and T4 endonuclease VII. Recently discovered enzymes, such as Endonuclease V from Thermotoga maritima and CEL I, have further advanced mismatch detection, due to a combination of useful properties. These include high specificity for a wide range of substrates, improved sensitivity for detecting a low level of mutants, and simple means of application. Standard approaches involve the PCR amplification of sample alleles using 5’-labeled primers and the size fractionation of digestion products by LIF electrophoresis. Such protocols, …
Analysis Of Bad Gene Expression In Oryza Sativa Using Qrtpcr, Timothy L. Fitzgerald, Daniel Le Waters, Robert J. Henry
Analysis Of Bad Gene Expression In Oryza Sativa Using Qrtpcr, Timothy L. Fitzgerald, Daniel Le Waters, Robert J. Henry
Adjunct Associate Professor Daniel LE Waters
Fragrance in rice (Oryza sativa), known to be primarily associated with grain 2-Acetyl-1-Pyrroline (2AP) concentration, is a highly valued trait. It has previously been determined that a non-functional betaine aldehyde dehydrogenase (BAD2) encoding gene homologue is responsible for fragrance in rice. It is hypothesized that in non-fragrant rice BAD2 catalyses the breakdown of a precursor to 2AP while the presence of a non-functional BAD2 encoding gene in fragrant varieties leads to an increase in the concentration of this precursor and a consequent increase in the concentration of 2AP. Functional BAD1 encoding genes have been identified in both fragrant and non-fragrant …
Generation Of Simple, Perfect Markers For Cereal Quality Traits, Louis Mt Bradbury, Daniel Le Waters, Robert J. Henry
Generation Of Simple, Perfect Markers For Cereal Quality Traits, Louis Mt Bradbury, Daniel Le Waters, Robert J. Henry
Adjunct Associate Professor Daniel LE Waters
Commercially important traits including fragrance and starch gelatinisation temperature (GT) are difficult phenotypes for breeders to asses. We recently identified polymorphisms that control these key rice quality traits. The annotated rice genome sequence used in combination with re-sequencing by PCR facilitated the discovery of these polymorphisms and the design of perfect molecular markers for each of these traits. In the absence of a genome sequence, larger mapping populations, a genome library and more sequencing would have been necessary. Although these traits result from different classes of polymorphism, fragrance is due to an eight base pair deletion while gelatinisation temperature variation …